5KEG

Crystal structure of APOBEC3A in complex with a single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 5KEG

Classification: HYDROLASE / DNA

Total Structure Weight: 27944.14


Macromolecule Entities
Molecule Chains Length Organism Details
DNA dC->dU-editing enzyme APOBEC-3A A 203 Homo sapiens EC#: 3.5.4 IUBMB
Mutation: E72A, C171A
Gene Name(s): APOBEC3A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*TP*CP*TP*T)-3') B 15 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.177
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 56.58 α = 90.00
b = 72.67 β = 90.00
c = 114.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-06-09
  • Released Date: 2017-05-10
  • Deposition author(s): Kouno, T., Hilbert, B.J., Silvas, T., Royer, W.E., Matsuo, H., Schiffer, C.A.

Revision History

  • 2017-09-13
    Type: Author supporting evidence